RetrogeneDB ID: | retro_cjac_2207 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:1074848..1075114(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CPSF4L | ||
| Ensembl ID: | ENSCJAG00000019911 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2207
TTTGAAACAGACAATGAGATGCAAAAGGGCACTGGGCTCCCTTCTTTCCAGGGCATGGAGAAGTCGGACTCAGCTGTGTG
CAACTTCTTCACTAAAGGGCTCTGTGAGAAAGGGAAACTGTCCCTTCCCAGTATGACCGAGGGGACAAGATGGTGGTGTA
TAAGCACCAGCTCTGGGGGCTGTGCAACAGGGGCGACCACCATAAGTTCCTGCCTCAGTATGACCTCACCAGGATGCCCA
AGTGCTACTCCTACTGCAAGTTCGGT
ORF - retro_cjac_2207 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 52.22 % |
| Parental protein coverage: | 53.94 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | FETDVETQKGTGLLPFQGMDNEACPSCCLGPSALASPGKF-CPFWHDRGEKTVVCKHWLRGLCKKGDPCK |
| FETD.E.QKGTGL..FQGM.......C......L...GK...P...DRG.K.VV.KH.L.GLC..GD..K | |
| Retrocopy | FETDNEMQKGTGLPSFQGMEKSDSAVCNFFTKGLCEKGKL<VPSQYDRGDKMVVYKHQLWGLCNRGDHHK |
| Parental | FLHQCDLTRRPECCFYSTFG |
| FL.Q.DLTR.P.C..Y..FG | |
| Retrocopy | FLPQYDLTRMPKCYSYCKFG |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP051959_colon | 0 .00 RPM | 0 .33 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .42 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .40 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .22 RPM |
| SRP051959_lung | 0 .00 RPM | 0 .42 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .48 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .35 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .44 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2207 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2207 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2207 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000019911 | 1 retrocopy |
retro_cjac_2207 ,
|
| Myotis lucifugus | ENSMLUG00000009617 | 2 retrocopies | |
| Monodelphis domestica | ENSMODG00000025672 | 1 retrocopy |